#!/bin/bash
# (Assumes you are in the EXAMPLES directory that contains this file)
haploh_path="../bin/haploh"

# run sample example05 with TPM estimation
$haploh_path  --baf example05.bafs --phased example05.hapguess \
            --event_mb 20 --event_prevalence 0.1 \
            --random_seed 1234 \
            --destdir demonstration_output --max_iterations 5

# run sample example10 with fixed TPM and 3 event states
$haploh_path  --baf example10.bafs --phased example10.hapguess \
            --event_mb 20 --event_prevalence 0.1 \
            --tpm fixed --num_event_states 3 \
            --random_seed 1234 \
            --destdir demonstration_output --max_iterations 5 

# run sample example21 with TPM estimation and estimate excess haplotype
$haploh_path  --baf example21.bafs --phased example21.hapguess \
            --event_mb 20 --event_prevalence 0.1 \
            --hapid --switchprobs example21.switchprobs \
            --random_seed 1234 \
            --destdir demonstration_output --max_iterations 5
            
# run sample example05 with TPM estimation and a bogus array of thresholds
$haploh_path  --baf example05.bafs.threshold --phased example05.hapguess \
            --event_mb 20 --event_prevalence 0.1 \
            --random_seed 1234 \
            --destdir demonstration_output --max_iterations 5
            
# run sample example05 with TPM estimation using baf mean instead of median
$haploh_path  --baf example05.bafs --phased example05.hapguess \
            --event_mb 20 --event_prevalence 0.1 \
            --random_seed 1234 \
            --threshold mean \
            --destdir demonstration_output --max_iterations 5

